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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.api.service.IClassificationService;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMethodMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportTaxIncludedInMapper;
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import eu.etaxonomy.cdm.io.common.mapping.IMappingImport;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.validation.CentralAfricaFernsTaxonImportValidator;
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import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
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import eu.etaxonomy.cdm.model.description.PresenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.location.TdwgArea;
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import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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/**
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* @author a.mueller
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*/
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@Component
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public class CentralAfricaFernsTaxonRelationImport extends CentralAfricaFernsImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaFernsImportState>{
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private static final Logger logger = Logger.getLogger(CentralAfricaFernsTaxonRelationImport.class);
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private DbImportMapping<?,?> mapping;
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private static final String pluralString = "taxon relations";
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private static final String dbTableName = "[African pteridophytes]";
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private static final Class<?> cdmTargetClass = TaxonBase.class;
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private Map<String, UUID> nameCacheTaxonMap = new HashMap<String, UUID>();
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private Map<String, UUID> titleCacheTaxonMap = new HashMap<String, UUID>();
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private CentralAfricaFernsImportState state;
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public CentralAfricaFernsTaxonRelationImport(){
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super(pluralString, dbTableName, cdmTargetClass);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery()
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*/
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@Override
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protected String getIdQuery() {
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String strQuery = " SELECT [Taxon number] FROM " + dbTableName;;
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return strQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#getMapping()
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*/
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@Override
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protected DbImportMapping<?,?> getMapping() {
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if (mapping == null){
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mapping = new DbImportMapping();
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mapping.addMapper(DbImportMethodMapper.NewInstance(this, "createObject", ResultSet.class, CentralAfricaFernsImportState.class));
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mapping.addMapper(DbImportMethodMapper.NewInstance(this, "mapCommonName", ResultSet.class, CentralAfricaFernsImportState.class));
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mapping.addMapper(DbImportMethodMapper.NewInstance(this, "mapDistribution", ResultSet.class, CentralAfricaFernsImportState.class ));
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mapping.addMapper(DbImportMethodMapper.NewInstance(this, "mapEcology", ResultSet.class, CentralAfricaFernsImportState.class));
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}
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return mapping;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#getRecordQuery(eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportConfigurator)
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*/
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@Override
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protected String getRecordQuery(CentralAfricaFernsImportConfigurator config) {
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String strSelect = " SELECT * ";
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String strFrom = " FROM [African pteridophytes] as ap";
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String strWhere = " WHERE ( ap.[taxon number] IN (" + ID_LIST_TOKEN + ") )";
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String strOrderBy = " ORDER BY [Taxon number]";
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String strRecordQuery = strSelect + strFrom + strWhere + strOrderBy ;
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return strRecordQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#doInvoke(eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportState)
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*/
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@Override
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protected void doInvoke(CentralAfricaFernsImportState state) {
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this.state = state;
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fillTaxonMap();
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super.doInvoke(state);
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return;
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}
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/**
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* Fills the nameCache and the titleCache maps. The maps are used to find existing taxa
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* by titleCache or nameCache matching.
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* Matching may be implemented more sophisticated in future versions.
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*/
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private void fillTaxonMap() {
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List<String> propPath = Arrays.asList(new String []{"name"});
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List<Taxon> taxonList = (List)getTaxonService().list(Taxon.class, null, null, null, propPath );
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for (Taxon taxon : taxonList){
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NonViralName<?> nvn = CdmBase.deproxy(taxon.getName(), NonViralName.class);
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UUID uuid = taxon.getUuid();
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String nameCache = nvn.getNameCache();
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String titleCache = nvn.getTitleCache();
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nameCacheTaxonMap.put(nameCache, uuid);
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titleCacheTaxonMap.put(titleCache, uuid);
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
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*/
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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String nameSpace;
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Class<?> cdmClass;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
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try{
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Set<String> taxonIdSet = new HashSet<String>();
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// Set<String> referenceIdSet = new HashSet<String>();
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet, "Current");
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handleForeignKey(rs, taxonIdSet, "Taxon number");
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// handleForeignKey(rs, referenceIdSet, "PTRefFk");
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}
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//taxon map
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nameSpace = TAXON_NAMESPACE;
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cdmClass = TaxonBase.class;
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Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, taxonIdSet, nameSpace);
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result.put(nameSpace, taxonMap);
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//reference map
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this.sourceReference = getFernsSourceReference(state);
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// nameSpace = "Reference";
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// cdmClass = Reference.class;
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// Map<String, Person> referenceMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(Person.class, teamIdSet, nameSpace);
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// result.put(Reference.class, referenceMap);
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} catch (SQLException e) {
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throw new RuntimeException(e);
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}
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)
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*/
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@Override
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public TaxonBase createObject(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException {
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TaxonBase<?> result = null;
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try {
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String status = rs.getString("Current/Synonym");
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String taxonNumber = rs.getString("Taxon number");
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state.setTaxonNumber(taxonNumber);
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if ("s".equalsIgnoreCase(status)){
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//synonym
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result = handleSynonym(rs, state);
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}else{
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//accepted Taxon
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result = handleTaxon(rs, state);
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}
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return result;
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} catch (Exception e) {
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e.printStackTrace();
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return result;
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}
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}
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/**
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* Class to store all epithets of the database record. Maybe extended with business logic.
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*/
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private class Epithets{
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private String orderName;
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private String subOrderName;
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private String familyName;
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private String subFamilyName;
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private String tribusName;
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private String subTribusName;
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private String sectionName;
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private String subsectionName;
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private String genusName;
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private String subGenusName;
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private String seriesName;
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private String specificEpithet;
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private String subspeciesName;
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private String varietyName;
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private String subVariety;
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private String formaName;
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private String subFormaName;
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}
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/**
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* Handles records with status synonym. A synonym relationship to the accepted taxon
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* is created.
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* @param rs
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* @param state
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* @return
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* @throws SQLException
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*/
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private Synonym handleSynonym(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException {
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String accTaxonId = rs.getString("Current");
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String nomRemarksString = rs.getString("Current/Synonym");
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String synonymId = state.getTaxonNumber();
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Synonym synonym = (Synonym)state.getRelatedObject(TAXON_NAMESPACE, synonymId);
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if (synonym == null){
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logger.warn ("Synonym ("+synonymId+")not found.");
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return null;
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}
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TaxonBase<?> taxonBase = CdmBase.deproxy(state.getRelatedObject(TAXON_NAMESPACE, accTaxonId), TaxonBase.class);
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if (taxonBase != null){
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if (taxonBase.isInstanceOf(Taxon.class)){
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Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
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SynonymRelationship rel = taxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF());
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if ("p.p.".equalsIgnoreCase(nomRemarksString)){
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rel.setProParte(true);
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}
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}else{
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logger.warn("Accepted taxon (" + accTaxonId + ") for synonym (" + synonymId +") is not of type 'Current'");
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}
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}else{
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logger.warn("Taxon (" + accTaxonId + ") not found for synonym (" + synonymId +")");
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}
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return synonym;
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}
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/**
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* Handles all records with status 'current'. Creates parent-child relationships to the
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* higher taxa. Uses a complex algorithm to reuse existing higher taxa.
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* @param rs
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* @param state
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* @return
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* @throws SQLException
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*/
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private Taxon handleTaxon(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException {
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String taxonNumber = rs.getString("Taxon number");
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Taxon child = (Taxon)state.getRelatedObject(TAXON_NAMESPACE, taxonNumber);
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if (child == null){
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logger.warn("Taxon does not exist: " + taxonNumber);
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return null;
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}
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Epithets epithets = new Epithets();
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epithets.orderName = rs.getString("Order name");
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epithets.subOrderName = rs.getString("Suborder name");
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epithets.familyName = rs.getString("Family name");
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epithets.subFamilyName = rs.getString("Subfamily name");
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epithets.tribusName = rs.getString("Tribus name");
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epithets.subTribusName = rs.getString("Subtribus name");
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epithets.sectionName = rs.getString("Section name");
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epithets.subsectionName = rs.getString("Subsection name");
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epithets.genusName = rs.getString("Genus name");
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epithets.subGenusName = rs.getString("Subgenus name");
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epithets.seriesName = rs.getString("Series name");
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epithets.specificEpithet = rs.getString("Specific epihet");
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epithets.subspeciesName = rs.getString("Subspecies name");
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epithets.varietyName = rs.getString("Variety name");
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epithets.subVariety = rs.getString("Subvariery");
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epithets.formaName = rs.getString("Forma name");
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epithets.subFormaName = rs.getString("Subforma");
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makeNextHigherTaxon(state, rs, child, epithets);
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return child;
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}
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/**
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* Adds recursively this taxon to the next higher taxon. If the taxon exists already
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* the relationship is not added again.<BR>
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* If the author is missing in the old taxon but not in the new taxon the
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* old taxon will get the new taxons author.(NOT VALID ANY MORE)<BR>
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* If authors differ a new taxon is created.<BR>
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* If a higher taxon exists the method is called recursively on this taxon.
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* @throws SQLException
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*/
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339
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private void makeNextHigherTaxon(CentralAfricaFernsImportState state, ResultSet rs, Taxon child, Epithets epithets) throws SQLException {
|
|
340
|
|
|
341
|
Taxon constructedHigherTaxon = constructNextHigherTaxon(state, rs, child, epithets);
|
|
342
|
Reference<?> citation = null;
|
|
343
|
String microcitation = null;
|
|
344
|
|
|
345
|
if (constructedHigherTaxon != null){
|
|
346
|
handleHigherTaxonMustExist(state, rs, child, epithets, constructedHigherTaxon, citation, microcitation);
|
|
347
|
}else{
|
|
348
|
//add taxon to tree if not yet added
|
|
349
|
if (child.getTaxonNodes().size() == 0){
|
|
350
|
makeTaxonomicallyIncluded(state, null, child, null, citation, microcitation);
|
|
351
|
}
|
|
352
|
}
|
|
353
|
}
|
|
354
|
|
|
355
|
|
|
356
|
|
|
357
|
/**
|
|
358
|
* Handles the case when the database record has data for a taxon of a higher rank
|
|
359
|
* than the <code>child</code> taxon's rank.
|
|
360
|
* @param state
|
|
361
|
* @param rs
|
|
362
|
* @param child
|
|
363
|
* @param epithets
|
|
364
|
* @param higherTaxon
|
|
365
|
* @param citation
|
|
366
|
* @param microcitation
|
|
367
|
* @throws SQLException
|
|
368
|
*/
|
|
369
|
private void handleHigherTaxonMustExist(CentralAfricaFernsImportState state, ResultSet rs, Taxon child, Epithets epithets, Taxon constructedHigherTaxon, Reference<?> citation, String microCitation) throws SQLException {
|
|
370
|
Taxon parentTaxon = getParent(child);
|
|
371
|
if (parentTaxon == null){
|
|
372
|
//if no parent taxon exists
|
|
373
|
Taxon existingTaxon = findExistingNonParentTaxon(state, constructedHigherTaxon);
|
|
374
|
if (existingTaxon != null){
|
|
375
|
//a taxon with same title cache or same name cache exists
|
|
376
|
parentTaxon = mergeExistingAndConstructedTaxon(state, existingTaxon, constructedHigherTaxon);
|
|
377
|
}else{
|
|
378
|
parentTaxon = constructedHigherTaxon;
|
|
379
|
}
|
|
380
|
makeTaxonomicallyIncluded(state, null, child, parentTaxon, citation, microCitation);
|
|
381
|
}else{
|
|
382
|
//parent taxon exists
|
|
383
|
if (namesMatch(parentTaxon, constructedHigherTaxon)){
|
|
384
|
//parents match
|
|
385
|
//TODO what if the higher taxonomy does not match
|
|
386
|
parentTaxon = mergeExistingAndConstructedTaxon(state, parentTaxon, constructedHigherTaxon);
|
|
387
|
}else if (compareRanks(parentTaxon, constructedHigherTaxon) != 0){
|
|
388
|
//ranks unequal
|
|
389
|
parentTaxon = handleUnequalRanks(parentTaxon, constructedHigherTaxon);
|
|
390
|
}else if (! nameCachesMatch(parentTaxon, constructedHigherTaxon)){
|
|
391
|
//nameCache not equal
|
|
392
|
parentTaxon = handleUnequalNameCaches(parentTaxon, constructedHigherTaxon);
|
|
393
|
}else if (! authorsMatch(parentTaxon, constructedHigherTaxon)){
|
|
394
|
//nameCache not equal
|
|
395
|
parentTaxon = handleUnequalAuthors(parentTaxon, constructedHigherTaxon);
|
|
396
|
}
|
|
397
|
}
|
|
398
|
//save the parent taxon, if it is new
|
|
399
|
if (parentTaxon == constructedHigherTaxon){
|
|
400
|
saveConstructedTaxon(state, constructedHigherTaxon);
|
|
401
|
}
|
|
402
|
makeNextHigherTaxon(state, rs, parentTaxon, epithets);
|
|
403
|
}
|
|
404
|
|
|
405
|
|
|
406
|
/**
|
|
407
|
* Merges author information of the constructed taxon into the existing taxon.
|
|
408
|
* Returns the existing taxon.
|
|
409
|
* @param state
|
|
410
|
* @param parentTaxon
|
|
411
|
* @param constructedHigherTaxon
|
|
412
|
*/
|
|
413
|
private Taxon mergeExistingAndConstructedTaxon(CentralAfricaFernsImportState state, Taxon existingTaxon, Taxon constructedTaxon) {
|
|
414
|
NonViralName<?> constructedName = CdmBase.deproxy(constructedTaxon.getName(), NonViralName.class);
|
|
415
|
NonViralName<?> existingName = CdmBase.deproxy(existingTaxon.getName(), NonViralName.class);
|
|
416
|
if (constructedName.hasAuthors()){
|
|
417
|
if (! existingName.hasAuthors()){
|
|
418
|
logger.warn(state.getTaxonNumber() + " - Constrcucted name ("+constructedName.getTitleCache()+") has authors but existing name ("+existingName.getTitleCache()+") has no authors");
|
|
419
|
}else if (! authorsMatch(constructedName, existingName)){
|
|
420
|
logger.warn(state.getTaxonNumber() + " - Constrcucted name ("+constructedName.getTitleCache()+") and existing name ("+existingName.getTitleCache()+") have different authors");
|
|
421
|
}else {
|
|
422
|
//authors match and are not null
|
|
423
|
}
|
|
424
|
}
|
|
425
|
// more?
|
|
426
|
return existingTaxon;
|
|
427
|
}
|
|
428
|
|
|
429
|
|
|
430
|
/**
|
|
431
|
* Strategy for the decision if an existing parent or a constructed higher taxon should
|
|
432
|
* be taken as parent in case that the authors of the name differ somehow.
|
|
433
|
* Current strategy: use existing parent if constructed higher taxon has no authors
|
|
434
|
* at all. Use constructed taxon otherwise.
|
|
435
|
* @param existingParentTaxon
|
|
436
|
* @param constructedHigherTaxon
|
|
437
|
* @return
|
|
438
|
*/
|
|
439
|
private Taxon handleUnequalAuthors(Taxon existingParentTaxon, Taxon constructedHigherTaxon) {
|
|
440
|
Taxon result;
|
|
441
|
BotanicalName existingName = CdmBase.deproxy(existingParentTaxon.getName(), BotanicalName.class);
|
|
442
|
BotanicalName constructedName = (BotanicalName)constructedHigherTaxon.getName();
|
|
443
|
//current strategy: if constructedName has no authors (and parentName has
|
|
444
|
if (! constructedName.hasAuthors()){
|
|
445
|
result = existingParentTaxon;
|
|
446
|
}else if (! existingName.hasAuthors()){
|
|
447
|
result = constructedHigherTaxon;
|
|
448
|
}else{
|
|
449
|
result = constructedHigherTaxon;
|
|
450
|
}
|
|
451
|
return result;
|
|
452
|
}
|
|
453
|
|
|
454
|
/**
|
|
455
|
* Strategy for the decision if an existing parent or a constructed higher taxon
|
|
456
|
* should be taken as parent in case that the name caches differ somehow.
|
|
457
|
* Current strategy: Not implemented. Always use constructed higher taxon.
|
|
458
|
* @param existingParentTaxon
|
|
459
|
* @param constructedHigherTaxon
|
|
460
|
* @return
|
|
461
|
*/
|
|
462
|
private Taxon handleUnequalNameCaches(Taxon parentTaxon, Taxon constructedHigherTaxon) {
|
|
463
|
BotanicalName parentName = CdmBase.deproxy(parentTaxon.getName(), BotanicalName.class);
|
|
464
|
BotanicalName constructedName = (BotanicalName)constructedHigherTaxon.getName();
|
|
465
|
logger.warn("handleUnequalNameCaches not yet implemented");
|
|
466
|
return constructedHigherTaxon;
|
|
467
|
}
|
|
468
|
|
|
469
|
|
|
470
|
/**
|
|
471
|
* Handles the case that the existing parent taxon and the constructed parent taxon
|
|
472
|
* have a diffent rank. Returns the constructedHigherTaxon if no common grand parent exists.
|
|
473
|
* @param parentTaxon
|
|
474
|
* @param constructedHigherTaxon
|
|
475
|
* @return
|
|
476
|
*/
|
|
477
|
private Taxon handleUnequalRanks(Taxon parentTaxon, Taxon constructedHigherTaxon) {
|
|
478
|
BotanicalName parentName = CdmBase.deproxy(parentTaxon.getName(), BotanicalName.class);
|
|
479
|
BotanicalName constructedName = (BotanicalName)constructedHigherTaxon.getName();
|
|
480
|
int compare = compareRanks(parentName, constructedName);
|
|
481
|
Taxon lowerTaxon = parentTaxon;
|
|
482
|
Taxon grandParentTaxon = constructedHigherTaxon;
|
|
483
|
if (compare < 0){
|
|
484
|
lowerTaxon = constructedHigherTaxon;
|
|
485
|
grandParentTaxon = parentTaxon;
|
|
486
|
}
|
|
487
|
Taxon commonGrandParent = checkIsGrandParent(lowerTaxon, grandParentTaxon);
|
|
488
|
if (commonGrandParent != null){
|
|
489
|
if (lowerTaxon == constructedHigherTaxon){
|
|
490
|
//TODO merge
|
|
491
|
logger.warn("Merge in between taxon not yet implemented");
|
|
492
|
}
|
|
493
|
}else{
|
|
494
|
return constructedHigherTaxon;
|
|
495
|
}
|
|
496
|
return lowerTaxon;
|
|
497
|
}
|
|
498
|
|
|
499
|
/**
|
|
500
|
* Tries to find a taxon which matches the constructed taxon but is not a parent
|
|
501
|
* taxon of the constructed taxon's child (condition will not be checked).
|
|
502
|
* Returns null if no such taxon exists.
|
|
503
|
* @param constructedHigherTaxon
|
|
504
|
* @param state
|
|
505
|
* @return
|
|
506
|
*/
|
|
507
|
private Taxon findExistingNonParentTaxon(CentralAfricaFernsImportState state, Taxon constructedHigherTaxon) {
|
|
508
|
BotanicalName constructedName = CdmBase.deproxy(constructedHigherTaxon.getName(), BotanicalName.class);
|
|
509
|
String titleCache = constructedName.getTitleCache();
|
|
510
|
String nameCache = constructedName.getNameCache();
|
|
511
|
UUID existingUuid = titleCacheTaxonMap.get(titleCache);
|
|
512
|
if (existingUuid == null){
|
|
513
|
existingUuid = nameCacheTaxonMap.get(nameCache);
|
|
514
|
}
|
|
515
|
Taxon relatedTaxon = null;
|
|
516
|
if (existingUuid != null){
|
|
517
|
relatedTaxon = state.getRelatedObject(HIGHER_TAXON_NAMESPACE, nameCache, Taxon.class);
|
|
518
|
if (relatedTaxon == null){
|
|
519
|
//TODO find for partition
|
|
520
|
relatedTaxon = (Taxon)getTaxonService().find(existingUuid);
|
|
521
|
if (relatedTaxon == null){
|
|
522
|
logger.info(state.getTaxonNumber() + " - Could not find existing name ("+nameCache+") in related objects map");
|
|
523
|
}else{
|
|
524
|
state.addRelatedObject(HIGHER_TAXON_NAMESPACE, nameCache, relatedTaxon);
|
|
525
|
}
|
|
526
|
}
|
|
527
|
}
|
|
528
|
return relatedTaxon;
|
|
529
|
}
|
|
530
|
|
|
531
|
/**
|
|
532
|
* Checks if a taxon is a grand parent of another taxon
|
|
533
|
* @param lowerTaxon
|
|
534
|
* @param higherTaxon
|
|
535
|
* @return
|
|
536
|
*/
|
|
537
|
private Taxon checkIsGrandParent(Taxon childTaxon, Taxon grandParentTaxon) {
|
|
538
|
BotanicalName lowerName = CdmBase.deproxy(childTaxon.getName(), BotanicalName.class);
|
|
539
|
BotanicalName higherName = CdmBase.deproxy(grandParentTaxon.getName(), BotanicalName.class);
|
|
540
|
|
|
541
|
//TODO was wenn lowerTaxon constructed ist
|
|
542
|
logger.warn("checkIsGrandParent not yet fully implemented");
|
|
543
|
Taxon nextParent = getParent(childTaxon);
|
|
544
|
if (namesMatch(nextParent, grandParentTaxon)){
|
|
545
|
//TODO which one to return? Merging ?
|
|
546
|
logger.warn("checkIsGrandParent(matching) not yet fully implemented");
|
|
547
|
return grandParentTaxon;
|
|
548
|
}else{
|
|
549
|
if (compareRanks(lowerName, higherName) >= 0){
|
|
550
|
return null;
|
|
551
|
}else{
|
|
552
|
return checkIsGrandParent(childTaxon, grandParentTaxon);
|
|
553
|
}
|
|
554
|
}
|
|
555
|
}
|
|
556
|
|
|
557
|
|
|
558
|
/**
|
|
559
|
* Checks if the name caches match.
|
|
560
|
* @param name1
|
|
561
|
* @param name2
|
|
562
|
* @return
|
|
563
|
*/
|
|
564
|
private boolean nameCachesMatch(BotanicalName name1, BotanicalName name2) {
|
|
565
|
return CdmUtils.nullSafeEqual(name1.getNameCache(), name2.getNameCache());
|
|
566
|
}
|
|
567
|
|
|
568
|
/**
|
|
569
|
* Checks if the name caches of the related names match.
|
|
570
|
*@param taxon1
|
|
571
|
* @param taxon2
|
|
572
|
* @return
|
|
573
|
*/
|
|
574
|
private boolean nameCachesMatch(Taxon taxon1, Taxon taxon2) {
|
|
575
|
BotanicalName name1 = CdmBase.deproxy(taxon1.getName(), BotanicalName.class);
|
|
576
|
BotanicalName name2 = CdmBase.deproxy(taxon2.getName(), BotanicalName.class);
|
|
577
|
return nameCachesMatch(name1, name2);
|
|
578
|
}
|
|
579
|
|
|
580
|
|
|
581
|
/**
|
|
582
|
* Checks if all authors match
|
|
583
|
* @param name1
|
|
584
|
* @param name2
|
|
585
|
* @return
|
|
586
|
*/
|
|
587
|
private boolean authorsMatch(NonViralName<?> name1, NonViralName<?> name2) {
|
|
588
|
String combinationAuthor1 = name1.computeCombinationAuthorNomenclaturalTitle();
|
|
589
|
String combinationAuthor2 = name2.computeCombinationAuthorNomenclaturalTitle();
|
|
590
|
String basionymAuthor1 = name1.computeBasionymAuthorNomenclaturalTitle();
|
|
591
|
String basionymAuthor2 = name2.computeBasionymAuthorNomenclaturalTitle();
|
|
592
|
String exCombinationAuthor1 = name1.computeExCombinationAuthorNomenclaturalTitle();
|
|
593
|
String exCombinationAuthor2 = name2.computeExCombinationAuthorNomenclaturalTitle();
|
|
594
|
String exBasionymAuthor1 = name1.computeExBasionymAuthorNomenclaturalTitle();
|
|
595
|
String exBasionymAuthor2 = name2.computeExBasionymAuthorNomenclaturalTitle();
|
|
596
|
boolean result =
|
|
597
|
CdmUtils.nullSafeEqual(combinationAuthor1, combinationAuthor2) &&
|
|
598
|
CdmUtils.nullSafeEqual(basionymAuthor1, basionymAuthor2) &&
|
|
599
|
CdmUtils.nullSafeEqual(exCombinationAuthor1, exCombinationAuthor2) &&
|
|
600
|
CdmUtils.nullSafeEqual(exBasionymAuthor1, exBasionymAuthor2);
|
|
601
|
return result;
|
|
602
|
}
|
|
603
|
|
|
604
|
/**
|
|
605
|
* Checks if all authors of the related names match.
|
|
606
|
* @param taxon1
|
|
607
|
* @param taxon2
|
|
608
|
* @return
|
|
609
|
*/
|
|
610
|
private boolean authorsMatch(Taxon taxon1, Taxon taxon2) {
|
|
611
|
BotanicalName name1 = CdmBase.deproxy(taxon1.getName(), BotanicalName.class);
|
|
612
|
BotanicalName name2 = CdmBase.deproxy(taxon2.getName(), BotanicalName.class);
|
|
613
|
return authorsMatch(name1, name2);
|
|
614
|
}
|
|
615
|
|
|
616
|
/**
|
|
617
|
* Compares ranks of 2 names.
|
|
618
|
* @param parentName
|
|
619
|
* @param constructedName
|
|
620
|
* @return
|
|
621
|
*/
|
|
622
|
private int compareRanks(BotanicalName name1, BotanicalName name2) {
|
|
623
|
return name1.getRank().compareTo(name2.getRank());
|
|
624
|
}
|
|
625
|
|
|
626
|
/**
|
|
627
|
* Compares the ranks of the according names.
|
|
628
|
* @param taxon1
|
|
629
|
* @param taxon2
|
|
630
|
* @return
|
|
631
|
*/
|
|
632
|
private int compareRanks(Taxon taxon1, Taxon taxon2) {
|
|
633
|
BotanicalName name1 = CdmBase.deproxy(taxon1.getName(), BotanicalName.class);
|
|
634
|
BotanicalName name2 = CdmBase.deproxy(taxon2.getName(), BotanicalName.class);
|
|
635
|
return compareRanks(name1, name2);
|
|
636
|
}
|
|
637
|
|
|
638
|
|
|
639
|
|
|
640
|
/**
|
|
641
|
* Checks if 2 names match.
|
|
642
|
* Current strategy: true, if ranks are equal, nameCaches match and authors match
|
|
643
|
* @param name1
|
|
644
|
* @param name2
|
|
645
|
* @return
|
|
646
|
*/
|
|
647
|
private boolean namesMatch(BotanicalName name1, BotanicalName name2) {
|
|
648
|
return compareRanks(name1, name2)==0 && nameCachesMatch(name1, name2) && authorsMatch(name1, name2);
|
|
649
|
}
|
|
650
|
|
|
651
|
/**
|
|
652
|
* Checks if the according names match.
|
|
653
|
* @see #namesMatch(BotanicalName, BotanicalName)
|
|
654
|
* @param taxon1
|
|
655
|
* @param taxon2
|
|
656
|
* @return
|
|
657
|
*/
|
|
658
|
private boolean namesMatch(Taxon taxon1, Taxon taxon2) {
|
|
659
|
BotanicalName name1 = CdmBase.deproxy(taxon1.getName(), BotanicalName.class);
|
|
660
|
BotanicalName name2 = CdmBase.deproxy(taxon2.getName(), BotanicalName.class);
|
|
661
|
return namesMatch(name1, name2);
|
|
662
|
}
|
|
663
|
|
|
664
|
|
|
665
|
/**
|
|
666
|
* Returns the only parent of the taxon. If not parent exists <code>null</code> is
|
|
667
|
* returned.
|
|
668
|
* TODO move to taxon class (with classification)
|
|
669
|
* @param child
|
|
670
|
* @return
|
|
671
|
* @throws IllegalStateException if taxon belongs to multiple states
|
|
672
|
*/
|
|
673
|
private Taxon getParent(Taxon child) {
|
|
674
|
int countNodes = child.getTaxonNodes().size();
|
|
675
|
if (countNodes < 1){
|
|
676
|
return null;
|
|
677
|
}else if (countNodes > 1){
|
|
678
|
throw new IllegalStateException("Multiple nodes exist for child taxon. This is an invalid state for this import.");
|
|
679
|
}else{
|
|
680
|
TaxonNode childNode = child.getTaxonNodes().iterator().next();
|
|
681
|
TaxonNode parentNode = childNode.getParent();
|
|
682
|
if (parentNode != null){
|
|
683
|
return parentNode.getTaxon();
|
|
684
|
}else{
|
|
685
|
return null;
|
|
686
|
}
|
|
687
|
}
|
|
688
|
}
|
|
689
|
|
|
690
|
|
|
691
|
/**
|
|
692
|
* Persists and saves the newly created taxon to the CDM store and to the look-up
|
|
693
|
* maps.
|
|
694
|
* @param state
|
|
695
|
* @param constructedHigherTaxon
|
|
696
|
* @return
|
|
697
|
*/
|
|
698
|
private Taxon saveConstructedTaxon(CentralAfricaFernsImportState state, Taxon constructedHigherTaxon) {
|
|
699
|
BotanicalName constructedName = CdmBase.deproxy(constructedHigherTaxon.getName(), BotanicalName.class);
|
|
700
|
String nameCache = constructedName.getNameCache();
|
|
701
|
String titleCache = constructedName.getTitleCache();
|
|
702
|
nameCacheTaxonMap.put(nameCache, constructedHigherTaxon.getUuid());
|
|
703
|
titleCacheTaxonMap.put(titleCache, constructedHigherTaxon.getUuid());
|
|
704
|
state.addRelatedObject(HIGHER_TAXON_NAMESPACE, nameCache, constructedHigherTaxon);
|
|
705
|
|
|
706
|
//persist
|
|
707
|
// Reference citation = state.getConfig().getSourceReference(); //throws nonUniqueObject exception
|
|
708
|
Reference<?> citation = null;
|
|
709
|
String id = state.getTaxonNumber() + "-" + constructedName.getRank().getTitleCache();
|
|
710
|
addOriginalSource(constructedName, id, NAME_NAMESPACE, citation);
|
|
711
|
addOriginalSource(constructedHigherTaxon, id, TAXON_NAMESPACE, citation);
|
|
712
|
getTaxonService().save(constructedHigherTaxon);
|
|
713
|
|
|
714
|
return constructedHigherTaxon;
|
|
715
|
}
|
|
716
|
|
|
717
|
|
|
718
|
//TODO use Mapper
|
|
719
|
/**
|
|
720
|
* Adds the parent child relationship. Creates and saves the classification if needed.
|
|
721
|
* Adds parent and child to the classification.
|
|
722
|
* @param state
|
|
723
|
* @param treeRefFk
|
|
724
|
* @param child
|
|
725
|
* @param parent
|
|
726
|
* @param citation
|
|
727
|
* @param microCitation
|
|
728
|
* @return
|
|
729
|
*/
|
|
730
|
private boolean makeTaxonomicallyIncluded(CentralAfricaFernsImportState state, Integer treeRefFk, Taxon child, Taxon parent, Reference citation, String microCitation){
|
|
731
|
String treeKey;
|
|
732
|
UUID treeUuid;
|
|
733
|
if (treeRefFk == null){
|
|
734
|
treeKey = "1"; // there is only one tree and it gets the map key '1'
|
|
735
|
treeUuid = state.getConfig().getClassificationUuid();
|
|
736
|
}else{
|
|
737
|
treeKey =String.valueOf(treeRefFk);
|
|
738
|
treeUuid = state.getTreeUuidByTreeKey(treeKey);
|
|
739
|
}
|
|
740
|
Classification tree = (Classification)state.getRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey);
|
|
741
|
if (tree == null){
|
|
742
|
IClassificationService service = state.getCurrentIO().getClassificationService();
|
|
743
|
tree = service.find(treeUuid);
|
|
744
|
if (tree == null){
|
|
745
|
String treeName = state.getConfig().getClassificationName();
|
|
746
|
tree = Classification.NewInstance(treeName);
|
|
747
|
tree.setUuid(treeUuid);
|
|
748
|
//FIXME tree reference
|
|
749
|
tree.setReference(citation);
|
|
750
|
service.save(tree);
|
|
751
|
}
|
|
752
|
state.addRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey, tree);
|
|
753
|
}
|
|
754
|
|
|
755
|
TaxonNode childNode;
|
|
756
|
if (parent != null){
|
|
757
|
childNode = tree.addParentChild(parent, child, citation, microCitation);
|
|
758
|
}else{
|
|
759
|
childNode = tree.addChildTaxon(child, citation, microCitation, null);
|
|
760
|
}
|
|
761
|
return (childNode != null);
|
|
762
|
}
|
|
763
|
|
|
764
|
|
|
765
|
/**
|
|
766
|
* Reasons if a higher taxon should exist. If it should exist it returns it as a new taxon.
|
|
767
|
* Returns null otherwise.
|
|
768
|
* @return
|
|
769
|
* @throws SQLException
|
|
770
|
*/
|
|
771
|
private Taxon constructNextHigherTaxon(CentralAfricaFernsImportState state, ResultSet rs, Taxon childTaxon, Epithets epithets) throws SQLException {
|
|
772
|
|
|
773
|
Taxon result = null;
|
|
774
|
BotanicalName childName = CdmBase.deproxy(childTaxon.getName(), BotanicalName.class);
|
|
775
|
Rank childRank = childName.getRank();
|
|
776
|
BotanicalName higherName;
|
|
777
|
higherName = handleInfraSpecific(childRank, epithets);
|
|
778
|
if (higherName.getRank() == null){
|
|
779
|
handleSpecies(childRank, higherName, epithets);
|
|
780
|
}
|
|
781
|
if (higherName.getRank() == null){
|
|
782
|
handleInfraGeneric(childRank, higherName, epithets);
|
|
783
|
}
|
|
784
|
if (higherName.getRank() == null){
|
|
785
|
handleUninomial(childRank, higherName, epithets);
|
|
786
|
}
|
|
787
|
|
|
788
|
if (higherName.getRank() != null){
|
|
789
|
result = Taxon.NewInstance(higherName, childTaxon.getSec());
|
|
790
|
//TODO correct??
|
|
791
|
setAuthor(higherName, rs, state.getTaxonNumber(), true);
|
|
792
|
// UUID uuid = higherName.getUuid();
|
|
793
|
// String name = higherName.getNameCache();
|
|
794
|
// taxonMap.put(name, uuid);
|
|
795
|
// state.addRelatedObject(HIGHER_TAXON_NAMESPACE, higherName.getNameCache(), result);
|
|
796
|
}
|
|
797
|
return result;
|
|
798
|
}
|
|
799
|
|
|
800
|
private BotanicalName handleInfraSpecific(Rank lowerTaxonRank, Epithets epithets) {
|
|
801
|
|
|
802
|
BotanicalName taxonName = BotanicalName.NewInstance(null);
|
|
803
|
Rank newRank = null;
|
|
804
|
|
|
805
|
if (StringUtils.isNotBlank(epithets.subFormaName) && lowerTaxonRank.isLower(Rank.SUBFORM())){
|
|
806
|
taxonName.setInfraSpecificEpithet(epithets.subFormaName);
|
|
807
|
newRank = Rank.SUBFORM();
|
|
808
|
}else if (StringUtils.isNotBlank(epithets.formaName) && lowerTaxonRank.isLower(Rank.FORM())){
|
|
809
|
taxonName.setInfraSpecificEpithet(epithets.formaName);
|
|
810
|
newRank = Rank.FORM();
|
|
811
|
}else if (StringUtils.isNotBlank(epithets.subVariety) && lowerTaxonRank.isLower(Rank.SUBVARIETY())){
|
|
812
|
taxonName.setInfraSpecificEpithet(epithets.subVariety);
|
|
813
|
newRank = Rank.SUBVARIETY();
|
|
814
|
}else if (StringUtils.isNotBlank(epithets.varietyName) && lowerTaxonRank.isLower(Rank.VARIETY())){
|
|
815
|
taxonName.setInfraSpecificEpithet(epithets.varietyName);
|
|
816
|
newRank = Rank.VARIETY();
|
|
817
|
}else if (StringUtils.isNotBlank(epithets.subspeciesName) && lowerTaxonRank.isLower(Rank.SUBSPECIES())){
|
|
818
|
taxonName.setInfraSpecificEpithet(epithets.subspeciesName);
|
|
819
|
newRank = Rank.SUBSPECIES();
|
|
820
|
}
|
|
821
|
|
|
822
|
if (newRank != null){
|
|
823
|
taxonName.setSpecificEpithet(epithets.specificEpithet);
|
|
824
|
taxonName.setGenusOrUninomial(epithets.genusName);
|
|
825
|
taxonName.setRank(newRank);
|
|
826
|
}
|
|
827
|
|
|
828
|
return taxonName;
|
|
829
|
}
|
|
830
|
|
|
831
|
private BotanicalName handleSpecies(Rank lowerTaxonRank, BotanicalName taxonName, Epithets epithets) {
|
|
832
|
Rank newRank = null;
|
|
833
|
|
|
834
|
if (StringUtils.isNotBlank(epithets.specificEpithet) && lowerTaxonRank.isLower(Rank.SPECIES())){
|
|
835
|
taxonName.setSpecificEpithet(epithets.specificEpithet);
|
|
836
|
newRank = Rank.SPECIES();
|
|
837
|
}
|
|
838
|
if (newRank != null){
|
|
839
|
taxonName.setGenusOrUninomial(epithets.genusName);
|
|
840
|
taxonName.setRank(newRank);
|
|
841
|
}
|
|
842
|
return taxonName;
|
|
843
|
}
|
|
844
|
|
|
845
|
private BotanicalName handleInfraGeneric(Rank lowerTaxonRank, BotanicalName taxonName, Epithets epithets) {
|
|
846
|
Rank newRank = null;
|
|
847
|
|
|
848
|
if (StringUtils.isNotBlank(epithets.seriesName) && lowerTaxonRank.isLower(Rank.SERIES())){
|
|
849
|
taxonName.setInfraGenericEpithet(epithets.seriesName);
|
|
850
|
newRank = Rank.SERIES();
|
|
851
|
}else if (StringUtils.isNotBlank(epithets.subsectionName) && lowerTaxonRank.isLower(Rank.SUBSECTION_BOTANY())){
|
|
852
|
taxonName.setInfraGenericEpithet(epithets.subsectionName);
|
|
853
|
newRank = Rank.SUBSECTION_BOTANY();
|
|
854
|
}else if (StringUtils.isNotBlank(epithets.sectionName) && lowerTaxonRank.isLower(Rank.SECTION_BOTANY())){
|
|
855
|
taxonName.setInfraGenericEpithet(epithets.sectionName);
|
|
856
|
newRank = Rank.SECTION_BOTANY();
|
|
857
|
}else if (StringUtils.isNotBlank(epithets.subGenusName) && lowerTaxonRank.isLower(Rank.SUBGENUS())){
|
|
858
|
taxonName.setInfraGenericEpithet(epithets.subGenusName);
|
|
859
|
newRank = Rank.SUBGENUS();
|
|
860
|
}
|
|
861
|
if (newRank != null){
|
|
862
|
taxonName.setGenusOrUninomial(epithets.genusName);
|
|
863
|
taxonName.setRank(newRank);
|
|
864
|
}
|
|
865
|
return taxonName;
|
|
866
|
}
|
|
867
|
|
|
868
|
|
|
869
|
|
|
870
|
private BotanicalName handleUninomial(Rank lowerTaxonRank, BotanicalName taxonName, Epithets epithets) {
|
|
871
|
|
|
872
|
Rank newRank = null;
|
|
873
|
if (StringUtils.isNotBlank(epithets.genusName) && lowerTaxonRank.isLower(Rank.GENUS())){
|
|
874
|
taxonName.setGenusOrUninomial(epithets.genusName);
|
|
875
|
newRank = Rank.GENUS();
|
|
876
|
}else if (StringUtils.isNotBlank(epithets.subTribusName) && lowerTaxonRank.isLower(Rank.SUBTRIBE())){
|
|
877
|
taxonName.setGenusOrUninomial(epithets.subTribusName);
|
|
878
|
newRank = Rank.SUBTRIBE();
|
|
879
|
}else if (StringUtils.isNotBlank(epithets.tribusName) && lowerTaxonRank.isLower(Rank.TRIBE())){
|
|
880
|
taxonName.setGenusOrUninomial(epithets.tribusName);
|
|
881
|
newRank = Rank.TRIBE();
|
|
882
|
}else if (StringUtils.isNotBlank(epithets.subFamilyName) && lowerTaxonRank.isLower(Rank.SUBFAMILY())){
|
|
883
|
taxonName.setGenusOrUninomial(epithets.subFamilyName);
|
|
884
|
newRank = Rank.SUBFAMILY();
|
|
885
|
}else if (StringUtils.isNotBlank(epithets.familyName) && lowerTaxonRank.isLower(Rank.FAMILY())){
|
|
886
|
taxonName.setGenusOrUninomial(epithets.familyName);
|
|
887
|
newRank = Rank.FAMILY();
|
|
888
|
}else if (StringUtils.isNotBlank(epithets.subOrderName) && lowerTaxonRank.isLower(Rank.SUBORDER())){
|
|
889
|
taxonName.setGenusOrUninomial(epithets.subOrderName);
|
|
890
|
newRank = Rank.SUBORDER();
|
|
891
|
}else if (StringUtils.isNotBlank(epithets.orderName) && lowerTaxonRank.isLower(Rank.ORDER())){
|
|
892
|
taxonName.setGenusOrUninomial(epithets.orderName);
|
|
893
|
newRank = Rank.ORDER();
|
|
894
|
}
|
|
895
|
taxonName.setRank(newRank);
|
|
896
|
return taxonName;
|
|
897
|
}
|
|
898
|
|
|
899
|
|
|
900
|
/**
|
|
901
|
* for internal use only, used by MethodMapper
|
|
902
|
*/
|
|
903
|
private TaxonBase mapCommonName(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException{
|
|
904
|
String taxonNumber = state.getTaxonNumber();
|
|
905
|
String commonNames = rs.getString("Common names");
|
|
906
|
TaxonBase<?> taxonBase = state.getRelatedObject(state.CURRENT_OBJECT_NAMESPACE, state.CURRENT_OBJECT_ID, TaxonBase.class);
|
|
907
|
if (StringUtils.isNotBlank(commonNames)){
|
|
908
|
Taxon taxon = getAcceptedTaxon(taxonBase);
|
|
909
|
if ( taxon != null ){
|
|
910
|
TaxonDescription description = getTaxonDescription(taxon, false, true);
|
|
911
|
String[] split = commonNames.split(",");
|
|
912
|
for (String commonNameString: split){
|
|
913
|
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString.trim(), Language.ENGLISH());
|
|
914
|
description.addElement(commonName);
|
|
915
|
}
|
|
916
|
}else{
|
|
917
|
logger.warn(taxonNumber + " - Accepted taxon for synonym can't be defined for common name. Synonym " + taxonBase.getName().getTitleCache());
|
|
918
|
}
|
|
919
|
}
|
|
920
|
return taxonBase;
|
|
921
|
}
|
|
922
|
|
|
923
|
|
|
924
|
/**
|
|
925
|
* for internal use only, used by MethodMapper
|
|
926
|
*/
|
|
927
|
private TaxonBase mapDistribution(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException{
|
|
928
|
try {
|
|
929
|
String taxonNumber = state.getTaxonNumber();
|
|
930
|
// logger.info(taxonNumber);
|
|
931
|
TaxonBase<?> taxonBase = state.getRelatedObject(state.CURRENT_OBJECT_NAMESPACE, state.CURRENT_OBJECT_ID, TaxonBase.class);
|
|
932
|
String countriesString = rs.getString("Distribution - Country");
|
|
933
|
String province = rs.getString("Distribution - Province");
|
|
934
|
String distributionDetailed = rs.getString("Distribution - detailed");
|
|
935
|
if (taxonBase != null){
|
|
936
|
TaxonNameBase<?,?> nameUsedInSource = taxonBase.getName();
|
|
937
|
Taxon taxon = getAcceptedTaxon(taxonBase);
|
|
938
|
if (taxon != null){
|
|
939
|
|
|
940
|
if (StringUtils.isNotBlank(countriesString) ){
|
|
941
|
makeCountries(state, taxonNumber, taxon, nameUsedInSource, countriesString, province, distributionDetailed);
|
|
942
|
}
|
|
943
|
makeProvince(taxon, province);
|
|
944
|
makeDistributionDetailed(taxon, distributionDetailed);
|
|
945
|
}else{
|
|
946
|
logger.warn(taxonNumber + " - Accepted taxon for synonym can't be defined for distribution. Synonym " + taxonBase.getName().getTitleCache());
|
|
947
|
}
|
|
948
|
}else{
|
|
949
|
logger.warn(" - " + taxonNumber + ": TaxonBase was null");
|
|
950
|
}
|
|
951
|
return taxonBase;
|
|
952
|
} catch (Exception e) {
|
|
953
|
e.printStackTrace();
|
|
954
|
return null;
|
|
955
|
}
|
|
956
|
}
|
|
957
|
|
|
958
|
|
|
959
|
/**
|
|
960
|
* for internal use only, used by MethodMapper
|
|
961
|
* @param commonNames
|
|
962
|
*/
|
|
963
|
private TaxonBase mapEcology(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException{
|
|
964
|
String taxonNumber = state.getTaxonNumber();
|
|
965
|
String ecologyString = rs.getString("Ecology");
|
|
966
|
TaxonBase<?> taxonBase = state.getRelatedObject(state.CURRENT_OBJECT_NAMESPACE, state.CURRENT_OBJECT_ID, TaxonBase.class);
|
|
967
|
if (StringUtils.isNotBlank(ecologyString)){
|
|
968
|
Taxon taxon = getAcceptedTaxon(taxonBase);
|
|
969
|
|
|
970
|
if (taxon != null){
|
|
971
|
TaxonDescription description = getTaxonDescription(taxon, false, true);
|
|
972
|
TextData ecology = TextData.NewInstance(Feature.ECOLOGY());
|
|
973
|
ecology.putText(Language.ENGLISH(), ecologyString.trim());
|
|
974
|
description.addElement(ecology);
|
|
975
|
}else{
|
|
976
|
logger.warn(taxonNumber + " - Accepted taxon for synonym can't be defined for ecology. Synonym " + taxonBase.getName().getTitleCache());
|
|
977
|
}
|
|
978
|
}
|
|
979
|
return taxonBase;
|
|
980
|
}
|
|
981
|
|
|
982
|
|
|
983
|
|
|
984
|
|
|
985
|
private void makeDistributionDetailed(Taxon taxon, String distributionDetailed) {
|
|
986
|
if (StringUtils.isNotBlank(distributionDetailed)){
|
|
987
|
TaxonDescription description = getTaxonDescription(taxon, false, true);
|
|
988
|
TextData distribution = TextData.NewInstance(Feature.DISTRIBUTION());
|
|
989
|
description.addElement(distribution);
|
|
990
|
distribution.putText(Language.ENGLISH(), distributionDetailed);
|
|
991
|
}
|
|
992
|
}
|
|
993
|
|
|
994
|
|
|
995
|
private void makeProvince(Taxon taxon, String province) {
|
|
996
|
if (StringUtils.isNotBlank(province)){
|
|
997
|
TaxonDescription description = getTaxonDescription(taxon, false, true);
|
|
998
|
TextData distribution = TextData.NewInstance(Feature.DISTRIBUTION());
|
|
999
|
description.addElement(distribution);
|
|
1000
|
distribution.putText(Language.ENGLISH(), province);
|
|
1001
|
}
|
|
1002
|
}
|
|
1003
|
|
|
1004
|
|
|
1005
|
/**
|
|
1006
|
* @param state
|
|
1007
|
* @param taxonNumber
|
|
1008
|
* @param taxonBase
|
|
1009
|
* @param countriesString
|
|
1010
|
*/
|
|
1011
|
private void makeCountries(CentralAfricaFernsImportState state, String taxonNumber, Taxon taxon, TaxonNameBase nameUsedInSource, String countriesString, String province, String distributionDetailed) {
|
|
1012
|
countriesString = countriesString.replaceAll("\\*", "");
|
|
1013
|
countriesString = countriesString.replace(" ", " ");
|
|
1014
|
countriesString = countriesString.replace(", endemic", " - endemic");
|
|
1015
|
countriesString = countriesString.replace("(endemic)", " - endemic");
|
|
1016
|
countriesString = countriesString.replace("(introduced)", " - introduced");
|
|
1017
|
countriesString = countriesString.replace("(naturalised)", " - naturalised");
|
|
1018
|
countriesString = countriesString.replace("Madagascar-", "Madagascar -");
|
|
1019
|
countriesString = countriesString.replace("Mah\u00e9", "Mahe");
|
|
1020
|
|
|
1021
|
String[] split = countriesString.split("[,;]");
|
|
1022
|
String remainingString = null;
|
|
1023
|
for (String countryString : split){
|
|
1024
|
countryString = CdmUtils.concat(", ", remainingString , countryString);
|
|
1025
|
if (countryString.matches(".*\\(.*") && ! countryString.matches(".*\\).*")){
|
|
1026
|
remainingString = countryString;
|
|
1027
|
continue;
|
|
1028
|
}
|
|
1029
|
remainingString = null;
|
|
1030
|
try {
|
|
1031
|
makeSingleCountry(state, taxonNumber, taxon, nameUsedInSource, countryString.trim());
|
|
1032
|
} catch (UndefinedTransformerMethodException e) {
|
|
1033
|
e.printStackTrace();
|
|
1034
|
}
|
|
1035
|
}
|
|
1036
|
}
|
|
1037
|
|
|
1038
|
|
|
1039
|
private void makeSingleCountry(CentralAfricaFernsImportState state, String taxonNumber, Taxon taxon, TaxonNameBase nameUsedInSource, String country) throws UndefinedTransformerMethodException {
|
|
1040
|
boolean areaDoubtful = false;
|
|
1041
|
Distribution distribution = Distribution.NewInstance(null, PresenceTerm.PRESENT());
|
|
1042
|
Reference<?> sourceReference = this.sourceReference;
|
|
1043
|
distribution.addSource(taxonNumber, "Distribution_Country", sourceReference, null, nameUsedInSource, null);
|
|
1044
|
NamedArea area = null;
|
|
1045
|
//empty
|
|
1046
|
if (StringUtils.isBlank(country)){
|
|
1047
|
return;
|
|
1048
|
}
|
|
1049
|
country = country.trim();
|
|
1050
|
//doubtful
|
|
1051
|
if (country.startsWith("?")){
|
|
1052
|
areaDoubtful = true;
|
|
1053
|
country = country.substring(1).trim();
|
|
1054
|
}
|
|
1055
|
//status
|
|
1056
|
country = makeCountryStatus(state, country, distribution);
|
|
1057
|
|
|
1058
|
//brackets
|
|
1059
|
country = makeCountryBrackets(state, taxonNumber, taxon, nameUsedInSource, country);
|
|
1060
|
String countryWithoutIslands = null;
|
|
1061
|
String countryWithoutDot = null;
|
|
1062
|
if (country.endsWith(" Isl.") || country.endsWith(" isl.") ){
|
|
1063
|
countryWithoutIslands = country.substring(0, country.length()-5);
|
|
1064
|
}
|
|
1065
|
if (country.endsWith(".")){
|
|
1066
|
countryWithoutDot = country.substring(0, country.length()-1);
|
|
1067
|
}
|
|
1068
|
if (country.endsWith("*")){
|
|
1069
|
country = country.substring(0, country.length()-1);
|
|
1070
|
}
|
|
1071
|
if (country.endsWith("Islands")){
|
|
1072
|
country = country.replace("Islands", "Is.");
|
|
1073
|
}
|
|
1074
|
|
|
1075
|
|
|
1076
|
//areas
|
|
1077
|
if (TdwgArea.isTdwgAreaLabel(country)){
|
|
1078
|
//tdwg
|
|
1079
|
area = TdwgArea.getAreaByTdwgLabel(country);
|
|
1080
|
}else if (TdwgArea.isTdwgAreaLabel(countryWithoutIslands)){
|
|
1081
|
//tdwg
|
|
1082
|
area = TdwgArea.getAreaByTdwgLabel(countryWithoutIslands);
|
|
1083
|
}else if (TdwgArea.isTdwgAreaLabel(countryWithoutDot)){
|
|
1084
|
//tdwg
|
|
1085
|
area = TdwgArea.getAreaByTdwgLabel(countryWithoutDot);
|
|
1086
|
}else if ( (area = state.getTransformer().getNamedAreaByKey(country)) != null) {
|
|
1087
|
//area already set
|
|
1088
|
}else if (WaterbodyOrCountry.isWaterbodyOrCountryLabel(country)){
|
|
1089
|
//iso
|
|
1090
|
area = WaterbodyOrCountry.getWaterbodyOrCountryByLabel(country);
|
|
1091
|
}else{
|
|
1092
|
//others
|
|
1093
|
NamedAreaLevel level = null;
|
|
1094
|
NamedAreaType areaType = null;
|
|
1095
|
|
|
1096
|
UUID uuid = state.getTransformer().getNamedAreaUuid(country);
|
|
1097
|
if (uuid == null){
|
|
1098
|
logger.error(taxonNumber + " - Unknown country: " + country);
|
|
1099
|
}
|
|
1100
|
area = getNamedArea(state, uuid, country, country, country, areaType, level);
|
|
1101
|
}
|
|
1102
|
|
|
1103
|
distribution.setArea(area);
|
|
1104
|
if (areaDoubtful == true){
|
|
1105
|
if (distribution.getStatus().equals(PresenceTerm.PRESENT())){
|
|
1106
|
distribution.setStatus(PresenceTerm.PRESENT_DOUBTFULLY());
|
|
1107
|
}
|
|
1108
|
}
|
|
1109
|
TaxonDescription description = getTaxonDescription(taxon, false, true);
|
|
1110
|
description.addElement(distribution);
|
|
1111
|
}
|
|
1112
|
|
|
1113
|
|
|
1114
|
|
|
1115
|
/**
|
|
1116
|
* @param state
|
|
1117
|
* @return
|
|
1118
|
*/
|
|
1119
|
private Reference<?> sourceReference = null;
|
|
1120
|
private Reference<?> getFernsSourceReference(CentralAfricaFernsImportState state) {
|
|
1121
|
// if (sourceReference == null || true){
|
|
1122
|
Reference<?> tmpReference = state.getConfig().getSourceReference();
|
|
1123
|
sourceReference = getReferenceService().find(tmpReference.getUuid());
|
|
1124
|
// }
|
|
1125
|
return sourceReference;
|
|
1126
|
}
|
|
1127
|
|
|
1128
|
|
|
1129
|
private String makeCountryBrackets(CentralAfricaFernsImportState state, String taxonNumber, Taxon taxon, TaxonNameBase<?,?> nameUsedInSource, String country) {
|
|
1130
|
String[] split = (country + " ").split("\\(.*\\)");
|
|
1131
|
if (split.length == 2){
|
|
1132
|
String bracket = country.substring(split[0].length()+1, country.indexOf(")"));
|
|
1133
|
country = split[0].trim();
|
|
1134
|
makeCountries(state, taxonNumber, taxon, nameUsedInSource, bracket, null, null);
|
|
1135
|
}else if (split.length ==1){
|
|
1136
|
//do nothing
|
|
1137
|
}else{
|
|
1138
|
logger.warn("Illegal length");
|
|
1139
|
}
|
|
1140
|
return country;
|
|
1141
|
}
|
|
1142
|
|
|
1143
|
private String makeCountryStatus(CentralAfricaFernsImportState state, String country, Distribution distribution) throws UndefinedTransformerMethodException {
|
|
1144
|
PresenceAbsenceTermBase<?> status = null;
|
|
1145
|
String[] split = country.split(" - ");
|
|
1146
|
|
|
1147
|
if (split.length == 2){
|
|
1148
|
country = split[0].trim();
|
|
1149
|
String statusString = split[1];
|
|
1150
|
statusString = statusString.replace(".", "");
|
|
1151
|
status = state.getTransformer().getPresenceTermByKey(statusString);
|
|
1152
|
if (status == null){
|
|
1153
|
logger.warn("No status found: "+ statusString);
|
|
1154
|
}
|
|
1155
|
// UUID uuid = null;
|
|
1156
|
// status = getPresenceTerm(state, uuid, statusString, statusString, null);
|
|
1157
|
}else if (split.length == 1){
|
|
1158
|
//nothing to do
|
|
1159
|
}else{
|
|
1160
|
logger.warn("Invalid length: " + split.length);
|
|
1161
|
}
|
|
1162
|
if (status != null){
|
|
1163
|
distribution.setStatus(status);
|
|
1164
|
}
|
|
1165
|
return country;
|
|
1166
|
}
|
|
1167
|
|
|
1168
|
|
|
1169
|
|
|
1170
|
|
|
1171
|
/* (non-Javadoc)
|
|
1172
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
1173
|
*/
|
|
1174
|
@Override
|
|
1175
|
protected boolean doCheck(CentralAfricaFernsImportState state){
|
|
1176
|
IOValidator<CentralAfricaFernsImportState> validator = new CentralAfricaFernsTaxonImportValidator();
|
|
1177
|
return validator.validate(state);
|
|
1178
|
}
|
|
1179
|
|
|
1180
|
/* (non-Javadoc)
|
|
1181
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
1182
|
*/
|
|
1183
|
@Override
|
|
1184
|
protected boolean isIgnore(CentralAfricaFernsImportState state){
|
|
1185
|
return ! state.getConfig().isDoRelTaxa();
|
|
1186
|
}
|
|
1187
|
|
|
1188
|
|
|
1189
|
|
|
1190
|
//************************ OLD **********************************************************
|
|
1191
|
|
|
1192
|
/**
|
|
1193
|
* Adds the higherTaxon authors to the existingHigherTaxon authors if the higherTaxon has authors and
|
|
1194
|
* the existingHigherTaxon has no authors.
|
|
1195
|
* Returns false if both taxa have authors and the authors differ from each other.
|
|
1196
|
* @param higherTaxon
|
|
1197
|
* @param existingHigherTaxon
|
|
1198
|
*/
|
|
1199
|
private boolean mergeAuthors_old(Taxon higherTaxon, Taxon existingHigherTaxon) {
|
|
1200
|
NonViralName<?> existingName = CdmBase.deproxy(higherTaxon.getName(), NonViralName.class);
|
|
1201
|
NonViralName<?> newName = CdmBase.deproxy(existingHigherTaxon.getName(), NonViralName.class);
|
|
1202
|
if (existingName == newName){
|
|
1203
|
return true;
|
|
1204
|
}
|
|
1205
|
if (! newName.hasAuthors()){
|
|
1206
|
return true;
|
|
1207
|
}
|
|
1208
|
if (! existingName.hasAuthors()){
|
|
1209
|
existingName.setCombinationAuthorTeam(newName.getCombinationAuthorTeam());
|
|
1210
|
existingName.setExCombinationAuthorTeam(newName.getExCombinationAuthorTeam());
|
|
1211
|
existingName.setBasionymAuthorTeam(newName.getBasionymAuthorTeam());
|
|
1212
|
existingName.setExBasionymAuthorTeam(newName.getExBasionymAuthorTeam());
|
|
1213
|
return true;
|
|
1214
|
}
|
|
1215
|
boolean authorsAreSame = true;
|
|
1216
|
authorsAreSame &= getNomTitleNz(existingName.getCombinationAuthorTeam()).equals(getNomTitleNz(newName.getCombinationAuthorTeam()));
|
|
1217
|
authorsAreSame &= getNomTitleNz(existingName.getExCombinationAuthorTeam()).equals(getNomTitleNz(newName.getExCombinationAuthorTeam()));
|
|
1218
|
authorsAreSame &= getNomTitleNz(existingName.getBasionymAuthorTeam()).equals(getNomTitleNz(newName.getBasionymAuthorTeam()));
|
|
1219
|
authorsAreSame &= getNomTitleNz(existingName.getExBasionymAuthorTeam()).equals(getNomTitleNz(newName.getExBasionymAuthorTeam()));
|
|
1220
|
return authorsAreSame;
|
|
1221
|
|
|
1222
|
|
|
1223
|
}
|
|
1224
|
|
|
1225
|
/**
|
|
1226
|
* Returns the nomenclatural title of the author. Returns empty string if author is <code>null</code> or
|
|
1227
|
* titleCache is <code>null</code>.
|
|
1228
|
* @param author
|
|
1229
|
* @return
|
|
1230
|
*/
|
|
1231
|
private String getNomTitleNz(INomenclaturalAuthor author) {
|
|
1232
|
if (author != null){
|
|
1233
|
return CdmUtils.Nz(author.getNomenclaturalTitle());
|
|
1234
|
}else{
|
|
1235
|
return "";
|
|
1236
|
}
|
|
1237
|
}
|
|
1238
|
|
|
1239
|
private Taxon getExistingHigherTaxon_old(Taxon child, Taxon higherTaxon) {
|
|
1240
|
int countNodes = child.getTaxonNodes().size();
|
|
1241
|
if (countNodes < 1){
|
|
1242
|
return null;
|
|
1243
|
}else if (countNodes > 1){
|
|
1244
|
throw new IllegalStateException("Multiple nodes exist for child taxon. This is an invalid state.");
|
|
1245
|
}else{
|
|
1246
|
TaxonNode childNode = child.getTaxonNodes().iterator().next();
|
|
1247
|
TaxonNode parentNode = childNode.getParent();
|
|
1248
|
if (parentNode != null){
|
|
1249
|
String existingParentTitle = parentNode.getTaxon().getName().getTitleCache();
|
|
1250
|
String newParentTitle = higherTaxon.getName().getTitleCache();
|
|
1251
|
if (existingParentTitle.equals(newParentTitle)){
|
|
1252
|
return parentNode.getTaxon();
|
|
1253
|
}
|
|
1254
|
}
|
|
1255
|
return null;
|
|
1256
|
}
|
|
1257
|
}
|
|
1258
|
|
|
1259
|
|
|
1260
|
|
|
1261
|
/**
|
|
1262
|
* Tests if this the child taxon already is a child of the higher taxon.
|
|
1263
|
* @param child
|
|
1264
|
* @param higherTaxon
|
|
1265
|
* @return
|
|
1266
|
*/
|
|
1267
|
private boolean includedRelationshipExists_Old(Taxon child, Taxon higherTaxon) {
|
|
1268
|
int countNodes = higherTaxon.getTaxonNodes().size();
|
|
1269
|
if (countNodes < 1){
|
|
1270
|
return false;
|
|
1271
|
}else if (countNodes > 1){
|
|
1272
|
throw new IllegalStateException("Multiple nodes exist for higher taxon. This is an invalid state.");
|
|
1273
|
}else{
|
|
1274
|
TaxonNode higherNode = higherTaxon.getTaxonNodes().iterator().next();
|
|
1275
|
return childExists_old(child, higherNode);
|
|
1276
|
}
|
|
1277
|
}
|
|
1278
|
|
|
1279
|
|
|
1280
|
|
|
1281
|
private boolean childExists_old(Taxon child, TaxonNode higherNode) {
|
|
1282
|
for (TaxonNode childNode : higherNode.getChildNodes()){
|
|
1283
|
String existingChildTitle = childNode.getTaxon().getName().getTitleCache();
|
|
1284
|
String newChildTitle = child.getName().getTitleCache();
|
|
1285
|
if (existingChildTitle.equals(newChildTitle)){
|
|
1286
|
return true;
|
|
1287
|
}
|
|
1288
|
}
|
|
1289
|
return false;
|
|
1290
|
}
|
|
1291
|
|
|
1292
|
|
|
1293
|
}
|